Contacts of the strand formed by residues 241 - 250 (chain A) in PDB entry 3NNJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE 3.0 3.6 - - - +
104A SER* 2.6 32.3 - - - -
105A VAL* 2.7 47.2 + - + +
106A GLU 3.7 1.5 + - - +
107A PRO 3.2 14.5 + - - -
109A HIS* 3.6 40.2 + - - +
111A GLY* 4.6 5.5 - - - -
138A ASP* 4.6 0.9 - - - -
146A GLY* 4.3 13.7 + - - +
230A SER* 4.4 15.4 - - - -
231A VAL 3.5 19.8 + - - -
232A PRO* 3.2 23.2 - - - +
233A LEU* 3.4 28.9 - - + +
240A LEU* 1.3 71.3 - - - +
242A ARG* 1.3 56.9 + - - +
243A ALA* 4.1 0.4 - - - -
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.4 22.2 - - - +
37A LEU* 5.1 8.1 - - - +
102A LEU* 5.0 4.5 - - + -
103A PHE 3.3 3.6 - - - -
104A SER* 4.0 15.7 - - - -
136A PRO* 3.5 2.1 - - - +
137A LEU* 2.5 77.8 + - + +
138A ASP* 2.4 47.1 + - - +
238A HIS* 5.2 0.8 - - - +
240A LEU* 4.2 19.7 + - + +
241A ARG* 1.3 75.0 - - - +
243A ALA* 1.3 56.9 + - - +
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.4 7.7 - - - +
103A PHE* 2.8 42.3 + - + +
134A TRP* 3.2 37.9 - - + +
135A ILE 3.2 11.4 - - - +
136A PRO* 4.1 2.0 - - + -
137A LEU* 4.1 1.7 - - - +
241A ARG 5.4 0.7 - - - +
242A ARG* 1.3 75.6 - - - +
244A PHE* 1.3 63.5 + - - +
245A VAL* 4.2 0.7 - - + -
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.6 26.0 - - + -
37A LEU* 3.9 24.2 - - + -
73A TYR* 3.9 28.0 - + + -
75A PHE* 4.6 0.7 - + - -
76A VAL* 3.8 26.5 - - + -
100A ASN* 5.0 0.7 - - + -
101A ALA 3.2 25.1 - - - -
102A LEU* 4.0 10.3 - - + -
133A ILE 3.2 3.8 - - - +
134A TRP* 3.4 2.1 - - - -
135A ILE* 2.8 52.6 + - + +
137A LEU* 3.6 33.4 - - + -
243A ALA* 1.3 72.5 - - - +
245A VAL* 1.3 62.6 + - - +
246A ILE* 4.0 7.6 - - + -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A HIS* 3.9 1.2 + - - +
100A ASN* 3.9 1.2 - - - -
101A ALA* 3.0 30.6 + - + +
103A PHE* 3.3 37.5 - - + -
132A SER* 4.3 21.5 - - - +
133A ILE 3.3 7.2 - - - +
134A TRP* 4.1 20.0 - - + -
222A PHE* 5.4 5.2 - - + -
243A ALA 5.1 0.4 - - - +
244A PHE* 1.3 77.7 - - - +
246A ILE* 1.3 63.9 + - - +
247A ARG* 3.8 11.6 + - + -
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Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.2 7.4 - - + -
80A ILE* 4.0 26.5 - - + -
97A ILE* 4.0 6.7 - - + -
99A HIS 3.4 3.8 - - - +
100A ASN* 3.2 38.1 - - + +
132A SER* 3.1 8.0 - - - -
133A ILE* 2.9 38.5 + - + +
135A ILE* 3.8 28.0 - - + -
244A PHE* 4.6 6.7 - - + -
245A VAL* 1.3 76.3 - - - +
247A ARG* 1.3 62.0 + - - +
248A LEU* 3.7 25.5 + - + +
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.8 0.7 - - - -
98A MSE 2.8 41.8 + - + +
99A HIS* 3.0 48.3 + - + +
101A ALA* 5.6 1.7 - - - +
120A SER* 3.0 36.6 + - - +
121A PHE* 3.9 24.5 - - + -
123A PHE* 3.5 14.0 - - + -
131A ALA 3.7 3.6 - - - -
132A SER* 4.1 6.5 - - - +
245A VAL* 3.8 11.6 + - + -
246A ILE* 1.3 73.6 - - - +
248A LEU* 1.3 56.6 + - - +
283A ASP* 2.7 44.2 + - - -
285A VAL* 3.8 8.2 - - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 4.6 0.4 - - + -
84A LEU* 4.2 11.9 - - + -
87A LEU* 4.6 1.8 - - + -
95A LEU* 4.4 23.3 - - + -
96A MSE 3.2 9.2 - - - +
97A ILE* 3.4 38.4 - - + +
98A MSE 4.4 0.2 - - - +
121A PHE* 3.7 1.9 - - - -
129A PHE* 5.0 0.2 - - - -
130A GLY* 3.6 1.0 - - - -
131A ALA 2.9 36.4 + - - +
133A ILE* 3.5 33.4 - - + -
221A PHE* 4.0 18.8 - - + -
246A ILE* 3.7 15.3 - - + +
247A ARG* 1.3 74.5 - - - +
249A VAL* 1.3 68.2 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.5 5.1 - - - -
96A MSE 2.8 45.5 + - + +
98A MSE 3.5 39.9 - - + -
121A PHE* 4.6 9.0 - - + -
123A PHE* 4.6 4.3 - - + -
124A THR* 4.4 8.1 - - + -
129A PHE* 3.8 12.3 - - - +
130A GLY* 4.7 0.2 - - - -
248A LEU* 1.3 80.3 - - - +
250A ASP* 1.3 66.8 + - - +
253A THR* 3.8 13.9 - - + +
302A LEU* 4.0 22.7 - - + -
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS* 3.7 14.9 + - + +
94A ASN* 2.9 37.3 + - - +
95A LEU* 4.6 1.3 - - - +
96A MSE 4.1 1.9 - - - +
129A PHE* 3.8 26.3 + - + -
249A VAL* 1.3 77.7 - - - +
251A TYR* 1.3 67.2 + - - +
252A ASP* 2.9 33.7 + - - +
253A THR* 2.8 33.3 + - - +
302A LEU* 5.9 0.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il